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Coot: Difference between revisions
→Assorted questions and answers (from the mailinglist)
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=Assorted questions and answers (from the mailinglist)= | =Assorted questions and answers (from the mailinglist)= | ||
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I am sure this exists somewhere through scripting in COOT, but can I apply NCS edits to only a subset of NCS copies? In other words, can I tell coot which are NCS related chains, and which aren't. I am working on this nightmarish case of asymmetrical homodimers, where the sequences are very similar, but the structures are not, so I need to tell coot which chains are actually related to each other. | I am sure this exists somewhere through scripting in COOT, but can I apply NCS edits to only a subset of NCS copies? In other words, can I tell coot which are NCS related chains, and which aren't. I am working on this nightmarish case of asymmetrical homodimers, where the sequences are very similar, but the structures are not, so I need to tell coot which chains are actually related to each other. | ||
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There is also a GUI to activate this feature under Extensions -> NCS. | There is also a GUI to activate this feature under Extensions -> NCS. | ||
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Description of problematic situation: I am using [[SHELXL]] to refine my 1.2 Å data and I am refining the hydrogen atoms. Subsequent rebuilding in coot is difficult though since hydrogens often does not "follow" when you do side chain rebuilding. For the moment I have quit transfering hydrogens to coot and add the hydrogens every refinement cycle, though it would be good I think if I could see them in coot without bothering about wrong positions. So these are my specific questions: | |||
Specific Q1: Using "edit chi angles" does not work properly. | |||
A: This fails because for chi angles Coot uses the Refmac dictionary to know what is connected to what (if it can). The work-around is to rename the refmac dictionary so Coot can't find it - which will force Coot to find bond by distance criteria. | |||
Specific Q2: Using "real space refine" does not work properly. | |||
A: Yes this fails. Hydrogens are named differently to SHELX hydrogens. In principal this could be made to work if the dictionary was reworked to use SHELX hydrogen names. This would also fix the chi angles problem too of course. | |||
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It should be noted that the answers ("A") are from Paul Emsley himself (and were maybe slightly edited). | |||